The aim of ADF MAGE-ML Tool is to provide a module for converting ADF files (a tab delimited file representing microarray design layout) into
MAGE-ML format, and for generating an ADF from an array design described in MAGE-ML format. The
module is build upon the ADF specifications and
using MAGE-Stk APIs (Java). MIAME-compliance
checking, a logging system, and integration of
LifeScience Identifier (LSID) specifications are
key components of the module. The module can be used via the command line or a graphical user
interface.

AGM Build is a molecular builder and
conformational editor. It can be used for
interactive model preparation for molecular
dynamics simulations, including association of
atom types and partial charges. It features
geometry editing, lattice building, building of
chain molecules (e.g. proteins), chains with
predetermined conformations, and charges and atom
types according to selected Force Field.

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

Analyze ECGs is a graphical data analysis tool for use on
analog input DAQ data, such as that of RTLab. It is
useful for opening the '.nds' file format produced by
RTLab's data acquisition program, DAQSystem (it can
also open regular ASCII files). Aside from being a
general-purpose multichannel analog data editing tool, it
also contains custom features useful for analyzing cardiac
data. However, it can be used for editing/viewing
general-purpose data as well. Additionally, this program
can convert '.nds' files to ASCII format data.

AntFlow builds upon Apache Ant to provide a new
approach to simplifying system automation that
uses pipelines of hot folders chained together to
perform a given task. Using XML, it associates an
automated task such as data transfer, encryption,
or XML processing with a directory on the local
system. Whenever a file is copied or written into
the hot folder, the associated task is executed
and the file is moved to the next hot folder in
the pipeline for further processing.

Arka provides a nice GUI for the gp package of command-line utilities for manipulation and display of DNA/RNA/protein sequences, the WU-BLAST and FASTA program families, and additional graphical tools for various aspects of sequence analysis (e.g., GC plots and 3D graphs). It provides editable and saveable windows for standard input, output and error, and a dialog for any command-line program with specifications in a configuration file.

Artemis is a DNA sequence viewer and annotation
tool that allows visualization of sequence
features and the results of analyses within the
context of the sequence, and its six-frame
translation. It can read and write complete EMBL
and GENBANK database entries or sequence in FASTA
or raw format. Extra sequence features can be in
EMBL, GENBANK, or GFF format.

Asymptopia Flashcard System uses Motif and LaTeX
to produce, manage, and use attractively formatted flashcards. You load some or all of your "collections" and set the timer for pop-up
frequency. The GUI interface and "Collection Manager" make creating and modifying flashcards as simple as pushing a single button. A knowledge of LaTeX is only required when entering special symbols.